[BiO BB] Extreme 3` EST Assembly

[Hulk Norris]

Hi,

I have started work on the clustering and assembly of 3` sequenced ESTs.
Because of the nature of the sequencing process we can be certain that each
EST represents the extreme 3` end of an expressed transcript.

In order to allow for incorrect base calling and determine which transcripts
are detected with greater frequency I wish to cluster and assemble these
ESTs to form consensus sequences and generate contigs.

My problem is that clustering and assembly software does not take into
account the fact that all the ESTs under investigation are confirmed extreme
3` and will assimilate genuine terminal 3` sequence into upstream positions
of longer transcripts in cases of alternative polyadenylation of a single
gene.

Does anyone have experience of similar problems or approaches?  Any help or
direction would be sincerely appreciated.

Regards,

Dr Hulk Norris
Principal Bioinformatician
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